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Advances in Plant Genomics and Genetics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 15 July 2024 | Viewed by 2309

Special Issue Editor

Special Issue Information

Dear Colleagues,

Salt stress, drought stress, high temperatures, and low temperatures are major abiotic stressors that can severely limit plant growth, distribution, and crop yield. The study of plant genetics has major economic impacts: many staple crops are genetically modified to increase yields and provide resistance to stress. Transcription factors have the ability to respond to changes in the external environment by regulating their own expression and employing the spatiotemporal specificity of gene expression to activate target genes. Next-generation sequencing (NGS) technologies accelerate crop improvement methods by enabling the rapid and cost-effective sequencing of entire genomes and transcriptomes.

This Special Issue will address a selection of recent research topics and current review articles in the field of plant genomics and genetics. Bioinformatics papers, up-to-date review articles, and commentaries are also welcome. This Special Issue is supervised by Dr. Hengling Wei and assisted by our Guest Editor's Assistant Editor, Dr. Shoujiang Sun (China Agricultural University, Beijing, China).

Dr. Hengling Wei
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plant genomics
  • plant genetics
  • abiotic stresses
  • salt resistance
  • genome
  • next-generation sequencing

Published Papers (3 papers)

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Research

13 pages, 3151 KiB  
Article
Fine Mapping of Candidate Gene Controlling Anthocyanin Biosynthesis for Purple Peel in Solanum melongena L.
by Kai Xiao, Feng Tan, Aidong Zhang, Yaru Zhou, Weimin Zhu, Chonglai Bao, Dingshi Zha and Xuexia Wu
Int. J. Mol. Sci. 2024, 25(10), 5241; https://doi.org/10.3390/ijms25105241 - 11 May 2024
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Abstract
Fruit color is an intuitive quality of horticultural crops that can be used as an evaluation criterion for fruit ripening and is an important factor affecting consumers’ purchase choices. In this study, a genetic population from the cross of green peel ‘Qidong’ and [...] Read more.
Fruit color is an intuitive quality of horticultural crops that can be used as an evaluation criterion for fruit ripening and is an important factor affecting consumers’ purchase choices. In this study, a genetic population from the cross of green peel ‘Qidong’ and purple peel ‘8 guo’ revealed that the purple to green color of eggplant peel is dominant and controlled by a pair of alleles. Bulked segregant analysis (BSA), SNP haplotyping, and fine genetic mapping delimited candidate genes to a 350 kb region of eggplant chromosome 10 flanked by markers KA2381 and CA8828. One ANS gene (EGP22363) was predicted to be a candidate gene based on gene annotation and sequence alignment of the 350-kb region. Sequence analysis revealed that a single base mutation of ‘T’ to ‘C’ on the exon green peel, which caused hydrophobicity to become hydrophilic serine, led to a change in the three-level spatial structure. Additionally, EGP22363 was more highly expressed in purple peels than in green peels. Collectively, EGP22363 is a strong candidate gene for anthocyanin biosynthesis in purple eggplant peels. These results provide important information for molecular marker-assisted selection in eggplants, and a basis for analyzing the regulatory pathways responsible for anthocyanin biosynthesis in eggplants. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics)
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19 pages, 5467 KiB  
Article
Insights into the Hormone-Regulating Mechanism of Adventitious Root Formation in Softwood Cuttings of Cyclocarya paliurus and Optimization of the Hormone-Based Formula for Promoting Rooting
by Yuan Tian, Wanxia Yang, Shiying Wan and Shengzuo Fang
Int. J. Mol. Sci. 2024, 25(2), 1343; https://doi.org/10.3390/ijms25021343 - 22 Jan 2024
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Abstract
Adventitious root (AR) formation is vital for successful cutting propagation in plants, while the dynamic regulation of phytohormones is viewed as one of the most important factors affecting AR formation. Cyclocarya paliurus, a hard-to-root plant, is faced with the bottleneck of cloning [...] Read more.
Adventitious root (AR) formation is vital for successful cutting propagation in plants, while the dynamic regulation of phytohormones is viewed as one of the most important factors affecting AR formation. Cyclocarya paliurus, a hard-to-root plant, is faced with the bottleneck of cloning its superior varieties in practice. In this study, ten treatments were designed to figure out the best hormone-based formula for promoting AR formation in softwood cuttings and explore their hormone-regulating mechanisms. Both the rooting process and the rooting parameters of the softwood cuttings were significantly affected by different hormone-based formulas (p < 0.05), while the greatest rooting rate (93%) and root quality index were achieved in the H3 formula (SR3:IR3 = 1:1). Significant differences in the measured phytohormone concentrations, as well as in their ratios, were detected among the cuttings sampled at various AR formation stages (p < 0.05), whereas the dynamics for each phytohormone varied greatly during AR formation. The transcriptome analysis showed 12,028 differentially expressed genes (DEGs) identified during the rooting process of C. paliurus cuttings, while the KEGG enrichment analysis indicated that a total of 20 KEGG terms were significantly enriched in all the comparison samples, with 253 DEGs detected in signal transduction. Furthermore, 19 genes with vital functions in regulating the hormone signaling pathway were identified by means of a WGCNA analysis. Our results not only optimize a hormone-based formula for improving the rooting of C. paliurus cuttings but also provide an insight into the hormonal regulatory network during AR formation in softwood C. paliurus cuttings. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics)
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17 pages, 16661 KiB  
Article
Association of a Specific OsCULLIN3c Haplotype with Salt Stress Responses in Local Thai Rice
by Bagus Herwibawa, Chakkree Lekklar, Supachitra Chadchawan and Teerapong Buaboocha
Int. J. Mol. Sci. 2024, 25(2), 1040; https://doi.org/10.3390/ijms25021040 - 15 Jan 2024
Viewed by 927
Abstract
We previously found that OsCUL3c is involved in the salt stress response. However, there are no definitive reports on the diversity of OsCUL3c in local Thai rice. In this study, we showed that the CUL3 group was clearly separated from the other CUL [...] Read more.
We previously found that OsCUL3c is involved in the salt stress response. However, there are no definitive reports on the diversity of OsCUL3c in local Thai rice. In this study, we showed that the CUL3 group was clearly separated from the other CUL groups; next, we focused on OsCUL3c, the third CUL3 of the CUL3 family in rice, which is absent in Arabidopsis. A total of 111 SNPs and 28 indels over the OsCUL3c region, representing 79 haplotypes (haps), were found. Haplotyping revealed that group I (hap A and hap C) and group II (hap B1 and hap D) were different mutated variants, which showed their association with phenotypes under salt stress. These results were supported by cis-regulatory elements (CREs) and transcription factor binding sites (TFBSs) analyses. We found that LTR, MYC, [AP2; ERF], and NF-YB, which are related to salt stress, drought stress, and the response to abscisic acid (ABA), have distinct positions and numbers in the haplotypes of group I and group II. An RNA Seq analysis of the two predominant haplotypes from each group showed that the OsCUL3c expression of the group I representative was upregulated and that of group II was downregulated, which was confirmed by RT-qPCR. Promoter changes might affect the transcriptional responses to salt stress, leading to different regulatory mechanisms for the expression of different haplotypes. We speculate that OsCUL3c influences the regulation of salt-related responses, and haplotype variations play a role in this regulation. Full article
(This article belongs to the Special Issue Advances in Plant Genomics and Genetics)
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